Target (protein/gene name): protein-tyrosine-phosphatase NCBI Gene # or RefSeq#:12602158 Protein ID (NP or XP #) or Wolbachia#:YP_006006958.1 , Locus tag: Y11_34591 Organism:Yersinia enterocolitica Etiologic Risk Group (see link below): Risk Group 2 (RG2) - Bacterial Agents Including
Background/Disease Information:
Yersiniosis is an infectious disease caused by a bacterium
Yersinia enterocolitica is most frequently associated with acute diarrhea, terminal ileitis
Belongs to the family of Enterobacteriaceae
Occurs in humans and animals such as cattle, deer, pigs, and birds
Common symptoms in children are fever, [[#|abdominal pain]], and diarrhea, which is often bloody.
Some uncomplicated cases can be resolve on their own without antibiotic treatment but in more severe infections, antibiotics such as doxycycline may be useful.
Washing your hands daily and avoiding raw or undercooked meats can also prevent this disease.
Structure Available (PDB or Homology model): http://www.pdb.org/pdb/explore/explore.do?structureId=3U96 -- PDB # or closest PDB entry if using homology model: 3U96 -- Query Coverage (if not direct match): N/A -- Max Ident (if not direct match): N/A
Primer design results for 'tail' primers (this is just 2 sequences): --- 093012: These are not 'Tail' primers. See protocol. - Dr. B
1 ATGACCACCTCTGCACTCTCTCACCCATCTCTGCTCC 37 20 TTATTCGAGGAAATAAGATTGGAGCTTTTCACGT 34
Figure 1: image of the TMpred graph withamino acid sequence
NCBI Gene # or RefSeq#:12602158
Protein ID (NP or XP #) or Wolbachia#:YP_006006958.1 ,
Locus tag: Y11_34591
Organism: Yersinia enterocolitica
Etiologic Risk Group (see link below): Risk Group 2 (RG2) - Bacterial Agents Including
Background/Disease Information:
Essentiality of this protein: http://www.ncbi.nlm.nih.gov/pubmed/9063884, http://go.galegroup.com/ps/retrieve.do?sgHitCountType=None&sort=DA-SORT&inPS=true&prodId=AONE&userGroupName=txshracd2598&tabID=T002&searchId=R1&resultListType=RESULT_LIST&contentSegment=&searchType=AdvancedSearchForm¤tPosition=1&contentSet=GALE|A9353389&&docId=GALE|A9353389&docType=GALE&role=
Complex of enzymes:
EC#: 3.1.3.48Link to BRENDA EC# page: http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-- http://www.ncbi.nlm.nih.gov/pubmed/15588980
-- http://www.sciencedirect.com/science/article/pii/S1046202304001653
-- List cost and quantity of substrate reagents and supplier
p-nitrophenyl phosphate (pNPP)- SIGMA $71.00
Structure Available (PDB or Homology model): http://www.pdb.org/pdb/explore/explore.do?structureId=3U96
-- PDB # or closest PDB entry if using homology model: 3U96
-- Query Coverage (if not direct match): N/A
-- Max Ident (if not direct match): N/A
Druggable Target (see Databases for this): Protein kinases, http://onlinelibrary.wiley.com/doi/10.1002/ddr.20362/abstract
Current Inhibitors: http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48
Expression Information (has it been expressed in bacterial cells): http://www.ch.embnet.org/cgi-bin/TMPRED_form_parser
Purification Method: http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48
Image of protein (PyMol or etc):
*Amino Acid Sequence:
http://www.ncbi.nlm.nih.gov/protein/318607573?from=1&to=265&report=fasta
length of your protein in Amino Acids: 265
Molecular Weight of your protein in kiloDaltons: http://web.expasy.org/cgi-bin/protparam/protparam
Molar Extinction coefficient of your protein at 280 nm wavelength:
*CDS Gene Sequence:
http://www.ncbi.nlm.nih.gov/nuccore/319801179?from=3578535&to=3579332&report=fasta
ATGACGACATCTGCTCTATCTCATCCTTCCCTATTGCCACTGGATGGGGGTATTAACTTCCGTGATCTCG
GTGGTAACGTCGTTGCAGATGGCCGGCGTATTAAGCGCGGGTTATTGTTTCGTTCAGGATCACTTGATCG
TTTGAGCACCAAAGATTGTGCTGTTCTTAGCAGCGGCTCTGTCGCTCAAATCCTTGATTACCGCGATGCG
GATGAAGTTCAGGCTAAGCCCGATATTGTGTGGCAAGGTGCCAGTTATCACAATATTCCAGCCAACCCAC
CCAGCAGTGAAGTTAACGCCAATCTGGAAAAACTGACTAACGAGACGTTAGCAACATTTGATGCCAGAGC
TTTCATGTTAGAGCTGTACCGTCGCCTGCCATTTAATAATCAAGCTTATAAACAGTTAGTCAGTTTGCTA
CAAAATAGTGCCTCACCAGAGCATGCCGCTGCTGGCGTGGTACAGCATTGTGCAGTCGGGAAAGACCGTA
CTGGAGTGGGTTCGGCTTTGGTGTTGTTTGCTTTAGGTGCTGATGAATCGACGGTATTGGAAGATTACCT
GTTGACTGAAACAACACTGGCACCTTTCCGTGAACACATGCTGGCGGAATTGGCACTAAAACTAAATTCT
CAGGCGCTAGGACAGTTTGCATTTGTGTTATCGGCTCGAGAAGAGTTTATTCAAACCGCACTGCGATGTA
TTCAAGAGCGTTACGGGAGCAGCGAGCAATGGCTACAGCAGGAATTTGGTCTTGGCAGAATTGAGCGCGA
AAAGTTGCAGTCATATTTCCTGGAGTAA
*CDS Gene Sequence (codon optimized) -
http://helixweb.nih.gov/tmp/dnaworks_1346436365p1699_22129/LOGFILE.txt
Total Size Of Gene ......... 798 nt
1 ATGACCACCTCTGCACTCTCTCACCCATCTCTGCTCCCGCTGGACGGTGGTATCAACTTC
61 CGTGATCTGGGTGGTAACGTTGTTGCGGACGGTCGTCGTATTAAACGTGGTCTGCTGTTC
121 CGCAGCGGTAGCCTGGACCGTCTGTCTACCAAAGACTGCGCTGTTCTCTCTAGCGGTTCT
181 GTTGCGCAGATCCTGGACTACCGTGACGCGGACGAAGTTCAGGCGAAACCGGACATCGTT
241 TGGCAGGGTGCGTCTTACCACAACATCCCGGCGAACCCGCCGTCTTCTGAAGTTAACGCG
301 AACCTGGAAAAACTCACCAACGAAACTCTGGCCACCTTCGACGCTCGTGCGTTCATGCTG
361 GAACTGTACCGTCGTCTGCCGTTCAACAACCAGGCGTACAAACAGCTGGTTTCTCTCCTG
421 CAGAACTCTGCGTCTCCGGAACACGCGGCTGCGGGTGTTGTTCAGCACTGCGCGGTTGGT
481 AAAGACCGTACCGGTGTTGGTTCTGCGCTCGTCCTGTTTGCCCTCGGTGCCGACGAATCT
541 ACCGTTCTGGAAGACTACCTGCTGACTGAGACCACCCTGGCGCCTTTTCGTGAGCACATG
601 CTCGCTGAACTGGCTCTGAAACTGAACTCTCAGGCGCTGGGTCAGTTCGCCTTCGTTCTG
661 TCTGCGCGTGAAGAATTCATCCAAACGGCCCTGCGTTGCATCCAGGAACGCTACGGTTCT
721 AGCGAACAGTGGCTGCAACAGGAATTCGGTCTGGGTCGTATCGAACGTGAAAAGCTCCAA 781 TCTTATTTCCTCGAATAA
*GC% Content for gene (codon optimized): 55.89%
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
https://docs.google.com/document/d/1CwiVxxmojEtiNaIdlgOHQzBxSHymG1XhwzuSz3lFHVI/edit
Primer design results for 'tail' primers (this is just 2 sequences): --- 093012: These are not 'Tail' primers. See protocol. - Dr. B
1 ATGACCACCTCTGCACTCTCTCACCCATCTCTGCTCC 37
20 TTATTCGAGGAAATAAGATTGGAGCTTTTCACGT 34